The obvious answer is in order to annex it, as he has done. The question is not about end but about means.
Invading with military force, holding a referendum under the guns of Russian troops, and announcing a result reminiscent of the results of Soviet "elections," has consequences that one would think Putin would prefer to avoid. My guess is that economic sanctions will not hurt him very much. The major costs have to do with the responses of other powers, in particular European powers. The two obvious ones are to reduce their dependence on Russian gas, which will reduce Russia's income from selling it, and to strengthen their military to be better able to respond to any future aggression.
The alternative, assuming that a sizable majority of the population of the Crimea wanted to become Russian, would have been to push for a referendum under Ukrainian rule with outside observers and win it. At that point, if the Ukraine refused to accept the outcome, Putin would have had a much stronger case for military action, if not in international law, which recognizes no general right of secession, at least in international politics and public opinion.
Several possible explanations of why he did not follow that policy occur to me:
1. He did not believe the Ukraine would be willing to hold such a referendum.
2. He was playing to a domestic audience, establishing his image as a forceful defender of Russians and Russian influence.
3. He plans to follow up by further aggression against the Ukraine, perhaps conditional on the western reaction to the first step.
If the final alternative is correct, it is hard to see any plausible response other than to permit him to defeat the Ukrainian military and replace the Ukrainian government and/or annex additional Ukrainian territory, or to support the Ukrainian military with European and U.S. troops. Neither looks very attractive.